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Series GSE76763 Query DataSets for GSE76763
Status Public on Jun 15, 2016
Title UMI-4C for quantitative and targeted chromosomal contact profiling
Organism Homo sapiens
Experiment type Other
Summary We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation.
 
Overall design We constructed UMI-4C profiles of 13 different genomic loci (viewpoints) in five different cell lines, in order to study the 3D chromatin contact maps of these selected loci. The coordinates for these viewpoints are: G1p1 chrX:48646542; baitG1_3_5kb chrX:48641393; bait_50kb chrX:48595987; bait_165kb chrX:48476525; ANK1 chr8:41654693; hbb_3HS chr11:5221346; hbb_HBB chr11:5248714; hbb_HBBP1_G1 chr11:5266532; HBB_HBE chr11:5292159; HBB_HS2 chr11:5301345; HBB_HS3 chr11:5306690; HBB_HS5 chr11:5313539; HBB_HBD chr11:5256597
 
Contributor(s) Schwartzman O, Tanay A
Citation(s) 27376768
Submission date Jan 12, 2016
Last update date May 15, 2019
Contact name Omer Schwartzman
Organization name Weizmann Institute of Science
Street address 234 Herzl Street
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (53)
GSM2037324 G1p1_B1_2_1_CMK_I1
GSM2037325 G1p1_B1_2_1_CMK_I2
GSM2037326 G1p1_B1_2_1_CMY_I1
Relations
BioProject PRJNA308557
SRA SRP068353

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE76763_RAW.tar 2.8 Mb (http)(custom) TAR (of TXT)
GSE76763_adj.G1_165kb_2_1_1.CMK_I1.txt.gz 17.4 Kb (ftp)(http) TXT
GSE76763_adj.G1_165kb_2_1_1.CMK_I2.txt.gz 25.4 Kb (ftp)(http) TXT
GSE76763_adj.G1_165kb_2_1_1.DND41_I1.txt.gz 15.8 Kb (ftp)(http) TXT
GSE76763_adj.G1_165kb_2_1_1.DND41_I2.txt.gz 17.6 Kb (ftp)(http) TXT
GSE76763_adj.G1_165kb_2_1_1.k562_I1.txt.gz 16.7 Kb (ftp)(http) TXT
GSE76763_adj.G1_165kb_2_1_1.k562_I2.txt.gz 18.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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